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X-ray structure of the Peroxisomal Targeting Signal 1 (PTS1) of Trypanosoma Cruzi PEX5 in complex with the PTS1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M MgCl2, 0.1 M Tris pH 8.5 and 30% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.331 α = 90 b = 69.936 β = 100.05 c = 71.106 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9686 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 48.22 95.9 0.959 3.7 2.8 35080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.539
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 48.22 33423 1657 95.81 0.19544 0.19262 0.1925 0.25284 0.2527 RANDOM 30.849
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.47 0.2 0.19 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.446 r_dihedral_angle_4_deg 18.949 r_dihedral_angle_3_deg 16.411 r_long_range_B_refined 7.387 r_dihedral_angle_1_deg 5.134 r_scbond_it 3.807 r_mcangle_it 3.558 r_mcbond_it 2.43 r_angle_refined_deg 1.429 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.446 r_dihedral_angle_4_deg 18.949 r_dihedral_angle_3_deg 16.411 r_long_range_B_refined 7.387 r_dihedral_angle_1_deg 5.134 r_scbond_it 3.807 r_mcangle_it 3.558 r_mcbond_it 2.43 r_angle_refined_deg 1.429 r_chiral_restr 0.111 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4804 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction AutoProcess data scaling PHASER phasing